Dear Amber users:
After reading relevant papers and the AMBER 9 manual chapters on LES
and REMD, I have a few
questions on the implementation of these kind of MD.
1. It seems to me tha LES method is relatively computationally cheaper
than REMD, since the latter usually requires square(Number of atoms)
independent replicas at different temperatures.When the loop regions is
bigger, that require quite a lot of replicas Is that right? Another question
pertaining to parallel computation of REMD is: if a REMD require N replicas,
does this mean at least N cpu should be used simultaneously??
2. As Dr. Simmerling has noted in
>
> Generation of accurate protein loop conformations through low-barrier
> molecular dynamics. Proteins. 2003 Jun 1;51(4) 577-90.
>
A soft-core potential energy was used. However, I did not find
documentation on this in the AMBER 9 manual. Does this option exist in this
distribution?
3. As a non-expert in Molecular dynamics, I am pretty confused with the
LES and REMD and various hybrid methods. If my goal is to refine the loop
structure of a homology model, which method is better to obtain a reasonable
loop folding with a reasonable computation effort? It seems to me that LES
is better since the convergent behavior of the copies will usually suggest a
reasonable fold.
4. As there is no LES tutorial in the AMBER site and documentation is
limited, It is a little bit difficult for me to grasp the LES method.
Moreover, the Moil-view webpage:
http://morita.chem.sunysb.edu/~carlos/moil-view.html is not reachable
right now. More comprehensive documentation or guidance is needed. Are there
any plans on this?
Thank you for your attention.
Xiaonan Zhang
Shanghai public health clinical center
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Received on Sun Aug 24 2008 - 06:07:05 PDT
